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fix: adjust import paths to re-organization

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This commit is contained in:
Moritz E. Beber 2022-10-05 13:40:43 +02:00
parent b407fbcdce
commit f5af9fd939
12 changed files with 41 additions and 41 deletions
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2
subworkflows/local/db_check.nf
View file

@ -3,7 +3,7 @@
//
include { DATABASE_CHECK } from '../../modules/local/database_check'
include { UNTAR } from '../../modules/nf-core/modules/untar/main'
include { UNTAR } from '../../modules/nf-core/untar/main'
workflow DB_CHECK {
take:

4
subworkflows/local/input_check.nf
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@ -2,8 +2,8 @@
// Check input samplesheet and get read channels
//
include { EIDO_VALIDATE } from '../../modules/nf-core/modules/eido/validate/main'
include { EIDO_CONVERT } from '../../modules/nf-core/modules/eido/convert/main'
include { EIDO_VALIDATE } from '../../modules/nf-core/eido/validate/main'
include { EIDO_CONVERT } from '../../modules/nf-core/eido/convert/main'
workflow INPUT_CHECK {
take:

8
subworkflows/local/longread_hostremoval.nf
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@ -2,10 +2,10 @@
// Remove host reads via alignment and export off-target reads
//
include { MINIMAP2_INDEX } from '../../modules/nf-core/modules/minimap2/index/main'
include { MINIMAP2_ALIGN } from '../../modules/nf-core/modules/minimap2/align/main'
include { SAMTOOLS_VIEW } from '../../modules/nf-core/modules/samtools/view/main'
include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/modules/samtools/bam2fq/main'
include { MINIMAP2_INDEX } from '../../modules/nf-core/minimap2/index/main'
include { MINIMAP2_ALIGN } from '../../modules/nf-core/minimap2/align/main'
include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main'
include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/samtools/bam2fq/main'
workflow LONGREAD_HOSTREMOVAL {
take:

6
subworkflows/local/longread_preprocessing.nf
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@ -2,9 +2,9 @@
// Process long raw reads with porechop
//
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
include { FILTLONG } from '../../modules/nf-core/modules/filtlong/main'
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
include { PORECHOP } from '../../modules/nf-core/porechop/main'
include { FILTLONG } from '../../modules/nf-core/filtlong/main'
workflow LONGREAD_PREPROCESSING {
take:

18
subworkflows/local/profiling.nf
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@ -2,15 +2,15 @@
// Run profiling
//
include { MALT_RUN } from '../../modules/nf-core/modules/malt/run/main'
include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/modules/megan/rma2info/main'
include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main'
include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main'
include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/metaphlan3/main'
include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/modules/diamond/blastx/main'
include { MOTUS_PROFILE } from '../../modules/nf-core/modules/motus/profile/main'
include { MALT_RUN } from '../../modules/nf-core/malt/run/main'
include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/megan/rma2info/main'
include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main'
include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/centrifuge/centrifuge/main'
include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/centrifuge/kreport/main'
include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/metaphlan3/metaphlan3/main'
include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main'
include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main'
workflow PROFILING {
take:

6
subworkflows/local/shortread_adapterremoval.nf
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@ -2,9 +2,9 @@
// Process short raw reads with AdapterRemoval
//
include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/modules/adapterremoval/main'
include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main'
include { CAT_FASTQ } from '../../modules/nf-core/modules/cat/fastq/main'
include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/adapterremoval/main'
include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/adapterremoval/main'
include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main'
workflow SHORTREAD_ADAPTERREMOVAL {

4
subworkflows/local/shortread_complexityfiltering.nf
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@ -2,8 +2,8 @@
// Check input samplesheet and get read channels
//
include { BBMAP_BBDUK } from '../../modules/nf-core/modules/bbmap/bbduk/main'
include { PRINSEQPLUSPLUS } from '../../modules/nf-core/modules/prinseqplusplus/main'
include { BBMAP_BBDUK } from '../../modules/nf-core/bbmap/bbduk/main'
include { PRINSEQPLUSPLUS } from '../../modules/nf-core/prinseqplusplus/main'
workflow SHORTREAD_COMPLEXITYFILTERING {
take:

4
subworkflows/local/shortread_fastp.nf
View file

@ -2,8 +2,8 @@
// Process short raw reads with FastP
//
include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/fastp/main'
include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/fastp/main'
workflow SHORTREAD_FASTP {
take:

4
subworkflows/local/shortread_hostremoval.nf
View file

@ -2,8 +2,8 @@
// Remove host reads via alignment and export off-target reads
//
include { BOWTIE2_BUILD } from '../../modules/nf-core/modules/bowtie2/build/main'
include { BOWTIE2_ALIGN } from '../../modules/nf-core/modules/bowtie2/align/main'
include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
include { BOWTIE2_ALIGN } from '../../modules/nf-core/bowtie2/align/main'
workflow SHORTREAD_HOSTREMOVAL {
take:

2
subworkflows/local/shortread_preprocessing.nf
View file

@ -5,7 +5,7 @@
include { SHORTREAD_FASTP } from './shortread_fastp'
include { SHORTREAD_ADAPTERREMOVAL } from './shortread_adapterremoval'
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
workflow SHORTREAD_PREPROCESSING {
take:

12
subworkflows/local/standardisation_profiles.nf
View file

@ -2,11 +2,11 @@
// Standardise output files e.g. aggregation
//
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/modules/krakentools/combinekreports/main'
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/modules/krakentools/combinekreports/main'
include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/modules/metaphlan3/mergemetaphlantables/main'
include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main'
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/krakentools/combinekreports/main'
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main'
include { MOTUS_MERGE } from '../../modules/nf-core/motus/merge/main'
workflow STANDARDISATION_PROFILES {
take:
@ -99,7 +99,7 @@ workflow STANDARDISATION_PROFILES {
ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS.out.versions )
// MetaPhlAn3
ch_profiles_for_metaphlan3 = ch_input_profiles.metaphlan3
.map { [it[0]['db_name'], it[1]] }
.groupTuple()

12
subworkflows/local/visualization_krona.nf
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@ -2,13 +2,13 @@
// Create Krona visualizations
//
include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_KRONA } from '../../modules/nf-core/modules/megan/rma2info/main'
include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/modules/kaiju/kaiju2krona/main'
include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_KRONA } from '../../modules/nf-core/megan/rma2info/main'
include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/kaiju/kaiju2krona/main'
include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/krakentools/kreport2krona/main'
include { KRONA_CLEANUP } from '../../modules/local/krona_cleanup'
include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/modules/krona/ktimporttext/main'
include { KRONA_KTIMPORTTAXONOMY } from '../../modules/nf-core/modules/krona/ktimporttaxonomy/main'
include { GUNZIP } from '../../modules/nf-core/modules/gunzip/main'
include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/krona/ktimporttext/main'
include { KRONA_KTIMPORTTAXONOMY } from '../../modules/nf-core/krona/ktimporttaxonomy/main'
include { GUNZIP } from '../../modules/nf-core/gunzip/main'
workflow VISUALIZATION_KRONA {
take: